3NWG | pdb_00003nwg

The crystal structure of a microcomparments protein from Desulfitobacterium hafniense DCB

PDB DOI: https://doi.org/10.2210/pdb3NWG/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Desulfitobacterium hafniense DCB-2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-09 Released: 2010-09-22
Deposition Author(s): Fan, Y., Volkart, L., Gu, M., Axen, S., Greenleaf, W.B., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.283 (Depositor), 0.264 (DCC)
R-Value Work:
0.223 (Depositor), 0.228 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3NWG

This is version 1.3 of the entry. See complete history.

Literature

Structure of a PduT homolog from a novel bacterial microcompartment

Greenleaf, W.B., Fan, Y., Axen, S., Volkart, L., Gu, M., Joachimiak, A., Kerfeld, C.

To be published.

Macromolecule Content

Total Structure Weight: 19.23 kDa
Atom Count: 1,341
Modeled Residue Count: 180
Deposited Residue Count: 182
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcompartments protein	A	182	Desulfitobacterium hafniense DCB-2	Mutation(s): 0 Gene Names: Dhaf_0360
UniProt
Find proteins for B8G1Q4 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8G1Q4 Go to UniProtKB: B8G1Q4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8G1Q4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.283 (Depositor), 0.264 (DCC)
R-Value Work: 0.223 (Depositor), 0.228 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.862	α = 90
b = 104.862	β = 90
c = 81.309	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-09-22

Deposition Author(s):

Greenleaf, W.B.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.